Multiple sequence alignment - TraesCS5D01G379200

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5D01G379200 chr5D 100.000 2848 0 0 1 2848 450372602 450375449 0.000000e+00 5260.0
1 TraesCS5D01G379200 chr5D 79.942 693 75 33 964 1647 450379571 450380208 4.330000e-123 451.0
2 TraesCS5D01G379200 chr5D 94.118 68 4 0 2337 2404 450374875 450374942 1.400000e-18 104.0
3 TraesCS5D01G379200 chr5D 94.118 68 4 0 2274 2341 450374938 450375005 1.400000e-18 104.0
4 TraesCS5D01G379200 chr5D 89.157 83 6 3 2261 2342 452555383 452555463 1.810000e-17 100.0
5 TraesCS5D01G379200 chr5D 86.420 81 10 1 2262 2341 281223200 281223280 1.410000e-13 87.9
6 TraesCS5D01G379200 chr5B 91.647 1245 71 22 728 1962 550320292 550321513 0.000000e+00 1692.0
7 TraesCS5D01G379200 chr5B 82.343 623 64 21 1034 1647 550337821 550338406 1.520000e-137 499.0
8 TraesCS5D01G379200 chr5B 88.950 181 18 2 2637 2815 550333262 550333442 3.690000e-54 222.0
9 TraesCS5D01G379200 chr5B 91.667 84 4 2 1428 1511 602483845 602483765 2.320000e-21 113.0
10 TraesCS5D01G379200 chr5B 90.476 84 5 2 1428 1511 602649036 602648956 1.080000e-19 108.0
11 TraesCS5D01G379200 chr5B 95.122 41 2 0 2808 2848 550334291 550334331 6.590000e-07 65.8
12 TraesCS5D01G379200 chr5A 91.582 1081 63 15 797 1877 569677154 569678206 0.000000e+00 1467.0
13 TraesCS5D01G379200 chr5A 85.000 540 41 19 1116 1647 569682995 569683502 1.960000e-141 512.0
14 TraesCS5D01G379200 chr5A 81.287 513 54 24 2339 2848 569680230 569680703 7.450000e-101 377.0
15 TraesCS5D01G379200 chr5A 91.667 84 4 2 1428 1511 610078770 610078690 2.320000e-21 113.0
16 TraesCS5D01G379200 chr5A 91.667 84 4 2 1428 1511 610185321 610185241 2.320000e-21 113.0
17 TraesCS5D01G379200 chr5A 89.744 78 6 2 2267 2342 513713982 513714059 6.490000e-17 99.0
18 TraesCS5D01G379200 chr4D 91.989 724 50 6 11 727 51300916 51301638 0.000000e+00 1009.0
19 TraesCS5D01G379200 chr4D 91.273 699 53 6 35 727 386434655 386435351 0.000000e+00 946.0
20 TraesCS5D01G379200 chr6D 91.425 723 53 7 11 727 278629517 278628798 0.000000e+00 983.0
21 TraesCS5D01G379200 chr6D 91.286 700 52 7 35 727 436640574 436639877 0.000000e+00 946.0
22 TraesCS5D01G379200 chr6D 80.843 261 43 7 2345 2599 80150566 80150825 6.220000e-47 198.0
23 TraesCS5D01G379200 chr6D 92.958 71 5 0 1422 1492 435351404 435351474 1.400000e-18 104.0
24 TraesCS5D01G379200 chr6D 86.813 91 9 1 1557 1647 435750347 435750434 6.490000e-17 99.0
25 TraesCS5D01G379200 chr6D 84.783 92 9 3 1557 1647 435831797 435831710 1.410000e-13 87.9
26 TraesCS5D01G379200 chr6D 75.281 178 28 11 2084 2256 316264254 316264088 1.420000e-08 71.3
27 TraesCS5D01G379200 chr7D 91.047 726 57 6 11 730 604991401 604990678 0.000000e+00 974.0
28 TraesCS5D01G379200 chr7D 91.273 699 53 6 35 727 394234328 394235024 0.000000e+00 946.0
29 TraesCS5D01G379200 chr7D 78.439 269 50 7 2337 2598 501466897 501467164 4.880000e-38 169.0
30 TraesCS5D01G379200 chr7D 72.500 520 101 31 2081 2578 164642141 164641642 2.300000e-26 130.0
31 TraesCS5D01G379200 chr7D 80.226 177 23 8 2099 2266 163568905 163569078 3.850000e-24 122.0
32 TraesCS5D01G379200 chr7D 90.667 75 7 0 2267 2341 430947256 430947330 1.810000e-17 100.0
33 TraesCS5D01G379200 chr7D 88.312 77 8 1 2267 2342 411309447 411309371 1.090000e-14 91.6
34 TraesCS5D01G379200 chr7A 91.136 722 57 5 11 727 722766958 722766239 0.000000e+00 972.0
35 TraesCS5D01G379200 chr3D 91.148 723 55 7 11 727 395522192 395522911 0.000000e+00 972.0
36 TraesCS5D01G379200 chr3D 76.779 267 46 6 2337 2598 438467508 438467253 4.950000e-28 135.0
37 TraesCS5D01G379200 chr1A 90.569 721 60 6 13 727 118556723 118557441 0.000000e+00 948.0
38 TraesCS5D01G379200 chr2D 76.727 550 82 33 2064 2599 19634231 19634748 6.050000e-67 265.0
39 TraesCS5D01G379200 chr2D 87.179 78 8 2 2267 2342 19634474 19634551 1.410000e-13 87.9
40 TraesCS5D01G379200 chr1D 82.900 269 39 7 2337 2599 435529064 435528797 4.740000e-58 235.0
41 TraesCS5D01G379200 chr1D 88.158 76 8 1 2267 2341 423924840 423924915 3.910000e-14 89.8
42 TraesCS5D01G379200 chr1D 87.179 78 8 2 2267 2342 435529071 435528994 1.410000e-13 87.9
43 TraesCS5D01G379200 chr4A 80.541 185 23 9 2076 2253 505497044 505496866 2.300000e-26 130.0
44 TraesCS5D01G379200 chr4A 85.849 106 10 3 2151 2251 737101896 737102001 1.080000e-19 108.0
45 TraesCS5D01G379200 chr4A 71.257 501 109 26 2081 2566 467254098 467253618 8.400000e-16 95.3
46 TraesCS5D01G379200 chr7B 78.788 198 31 7 2063 2253 685250877 685250684 3.850000e-24 122.0
47 TraesCS5D01G379200 chr7B 92.105 76 5 1 2182 2256 58873708 58873783 3.880000e-19 106.0
48 TraesCS5D01G379200 chr7B 76.536 179 31 9 2081 2252 320093172 320093346 1.410000e-13 87.9
49 TraesCS5D01G379200 chr7B 97.368 38 1 0 2337 2374 96414626 96414663 6.590000e-07 65.8
50 TraesCS5D01G379200 chr2B 78.392 199 31 7 2076 2266 471744189 471744383 4.980000e-23 119.0
51 TraesCS5D01G379200 chr6B 91.892 74 6 0 1422 1495 658403358 658403431 1.400000e-18 104.0
52 TraesCS5D01G379200 chrUn 87.952 83 8 2 1249 1330 76960998 76961079 2.340000e-16 97.1
53 TraesCS5D01G379200 chrUn 87.952 83 8 2 1249 1330 104042012 104041931 2.340000e-16 97.1
54 TraesCS5D01G379200 chr6A 86.667 90 9 1 1558 1647 582516992 582517078 2.340000e-16 97.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G379200 chr5D 450372602 450375449 2847 False 1822.666667 5260 96.078667 1 2848 3 chr5D.!!$F4 2847
1 TraesCS5D01G379200 chr5D 450379571 450380208 637 False 451.000000 451 79.942000 964 1647 1 chr5D.!!$F2 683
2 TraesCS5D01G379200 chr5B 550320292 550321513 1221 False 1692.000000 1692 91.647000 728 1962 1 chr5B.!!$F1 1234
3 TraesCS5D01G379200 chr5B 550333262 550338406 5144 False 262.266667 499 88.805000 1034 2848 3 chr5B.!!$F2 1814
4 TraesCS5D01G379200 chr5A 569677154 569683502 6348 False 785.333333 1467 85.956333 797 2848 3 chr5A.!!$F2 2051
5 TraesCS5D01G379200 chr4D 51300916 51301638 722 False 1009.000000 1009 91.989000 11 727 1 chr4D.!!$F1 716
6 TraesCS5D01G379200 chr4D 386434655 386435351 696 False 946.000000 946 91.273000 35 727 1 chr4D.!!$F2 692
7 TraesCS5D01G379200 chr6D 278628798 278629517 719 True 983.000000 983 91.425000 11 727 1 chr6D.!!$R1 716
8 TraesCS5D01G379200 chr6D 436639877 436640574 697 True 946.000000 946 91.286000 35 727 1 chr6D.!!$R4 692
9 TraesCS5D01G379200 chr7D 604990678 604991401 723 True 974.000000 974 91.047000 11 730 1 chr7D.!!$R3 719
10 TraesCS5D01G379200 chr7D 394234328 394235024 696 False 946.000000 946 91.273000 35 727 1 chr7D.!!$F2 692
11 TraesCS5D01G379200 chr7A 722766239 722766958 719 True 972.000000 972 91.136000 11 727 1 chr7A.!!$R1 716
12 TraesCS5D01G379200 chr3D 395522192 395522911 719 False 972.000000 972 91.148000 11 727 1 chr3D.!!$F1 716
13 TraesCS5D01G379200 chr1A 118556723 118557441 718 False 948.000000 948 90.569000 13 727 1 chr1A.!!$F1 714

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
463 471 0.452122 GCCATTTTCCAACGTCGACG 60.452 55.0 34.58 34.58 46.33 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2188 7400 0.0293 CGGCAGTTGTTGTTCTGGTG 59.971 55.0 0.0 0.0 32.94 4.17 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 3.794481 TGCAGCCCATTTGCATGT 58.206 50.000 0.00 0.00 45.89 3.21
62 63 1.108776 AGCCCATTTGCATGTGCTAG 58.891 50.000 6.55 0.00 41.84 3.42
343 348 0.767375 AGACTGTGACATGGGCAAGT 59.233 50.000 0.00 2.17 0.00 3.16
349 354 3.027170 GACATGGGCAAGTGTCGCG 62.027 63.158 0.00 0.00 35.85 5.87
372 377 0.832135 TCAAGACGTGGAGGCCTTCT 60.832 55.000 13.68 5.19 0.00 2.85
418 423 0.472161 TGTACACACTGGGCCCACTA 60.472 55.000 24.45 0.00 0.00 2.74
431 437 0.962489 CCCACTAGCCATAGAGTCGG 59.038 60.000 0.00 0.00 32.93 4.79
463 471 0.452122 GCCATTTTCCAACGTCGACG 60.452 55.000 34.58 34.58 46.33 5.12
499 507 7.459444 TGTGGGAAAAATAATAATTCAAGGGGT 59.541 33.333 0.00 0.00 0.00 4.95
552 562 3.362262 CCTTCGGGTCACTGACGA 58.638 61.111 3.04 0.00 32.65 4.20
554 564 1.658114 CTTCGGGTCACTGACGACA 59.342 57.895 3.04 0.00 37.66 4.35
605 615 3.788766 GCTTGGGCGTACACAGCG 61.789 66.667 0.00 0.00 35.00 5.18
606 616 3.118454 CTTGGGCGTACACAGCGG 61.118 66.667 0.00 0.00 35.00 5.52
639 649 1.577328 ATTTGCACGTCCGAGCCAAG 61.577 55.000 6.65 0.00 0.00 3.61
655 665 2.685897 GCCAAGTTGTTACACCAGTTCA 59.314 45.455 1.45 0.00 0.00 3.18
683 693 3.888323 TGCCACAAGTTCTAGCATCAAAA 59.112 39.130 0.00 0.00 0.00 2.44
731 741 5.131784 ACCACCGGTGTAATTGACTAAAAA 58.868 37.500 31.80 0.00 32.98 1.94
764 774 0.603569 ACTGGATAATAGGCGCTCCG 59.396 55.000 7.64 4.53 37.47 4.63
765 775 0.888619 CTGGATAATAGGCGCTCCGA 59.111 55.000 7.64 0.00 37.47 4.55
768 778 3.093814 TGGATAATAGGCGCTCCGATAA 58.906 45.455 7.64 0.00 37.47 1.75
815 826 0.982673 GCTGTCGCTAACGTGTACTG 59.017 55.000 0.00 0.00 41.18 2.74
849 860 4.414999 CATATGAATGCGTCCAATGGAG 57.585 45.455 0.27 0.00 29.39 3.86
960 971 1.134640 ACGCACTTGTACTGGTGTCAA 60.135 47.619 16.00 0.00 36.03 3.18
1026 1037 0.604578 TAACCACCTGTAGTCGCACC 59.395 55.000 0.00 0.00 0.00 5.01
1029 1040 1.666011 CACCTGTAGTCGCACCTGT 59.334 57.895 0.00 0.00 0.00 4.00
1030 1041 0.033504 CACCTGTAGTCGCACCTGTT 59.966 55.000 0.00 0.00 0.00 3.16
1061 4598 2.738846 ACTCGCAGCAGTTCAATACTTG 59.261 45.455 0.00 0.00 33.85 3.16
1071 4608 5.335583 GCAGTTCAATACTTGCACAACCATA 60.336 40.000 0.00 0.00 33.85 2.74
1072 4609 6.086222 CAGTTCAATACTTGCACAACCATAC 58.914 40.000 0.00 0.00 33.85 2.39
1073 4610 5.767665 AGTTCAATACTTGCACAACCATACA 59.232 36.000 0.00 0.00 31.29 2.29
1074 4611 5.621197 TCAATACTTGCACAACCATACAC 57.379 39.130 0.00 0.00 0.00 2.90
1075 4612 5.066593 TCAATACTTGCACAACCATACACA 58.933 37.500 0.00 0.00 0.00 3.72
1076 4613 5.709631 TCAATACTTGCACAACCATACACAT 59.290 36.000 0.00 0.00 0.00 3.21
1077 4614 5.818136 ATACTTGCACAACCATACACATC 57.182 39.130 0.00 0.00 0.00 3.06
1104 4641 1.065928 CCTGTAGATCGACCGGTGC 59.934 63.158 14.63 2.29 0.00 5.01
1112 4649 2.552585 ATCGACCGGTGCACGTAAGG 62.553 60.000 14.63 13.54 46.39 2.69
1344 4881 1.340248 TCGGTGAGTTCAAGGACAGAC 59.660 52.381 0.00 0.00 0.00 3.51
1364 4901 1.673033 CCTGCCTGCCGCTATATACAC 60.673 57.143 0.00 0.00 38.78 2.90
1365 4902 1.000843 CTGCCTGCCGCTATATACACA 59.999 52.381 0.00 0.00 38.78 3.72
1709 5255 1.274167 TGTTCGGTCAAAGCTCGGTAT 59.726 47.619 0.00 0.00 0.00 2.73
1733 5283 0.023732 CGTACTTCTGCATGCGTTCG 59.976 55.000 14.09 10.32 0.00 3.95
1833 5388 7.596749 GTACATGTATTTGTACTGAAGTGCT 57.403 36.000 9.18 0.00 45.48 4.40
1834 5389 8.697846 GTACATGTATTTGTACTGAAGTGCTA 57.302 34.615 9.18 0.00 45.48 3.49
1835 5390 9.146984 GTACATGTATTTGTACTGAAGTGCTAA 57.853 33.333 9.18 0.00 45.48 3.09
1836 5391 8.615878 ACATGTATTTGTACTGAAGTGCTAAA 57.384 30.769 0.00 0.83 31.04 1.85
1837 5392 9.062524 ACATGTATTTGTACTGAAGTGCTAAAA 57.937 29.630 0.00 0.00 31.04 1.52
1838 5393 9.329913 CATGTATTTGTACTGAAGTGCTAAAAC 57.670 33.333 0.00 0.00 31.04 2.43
1839 5394 7.867752 TGTATTTGTACTGAAGTGCTAAAACC 58.132 34.615 0.00 0.00 31.04 3.27
1877 5432 5.341196 GCGCTCGTTTATATTTGTGTTTTGT 59.659 36.000 0.00 0.00 0.00 2.83
1878 5433 6.520447 GCGCTCGTTTATATTTGTGTTTTGTA 59.480 34.615 0.00 0.00 0.00 2.41
1879 5434 7.252865 GCGCTCGTTTATATTTGTGTTTTGTAG 60.253 37.037 0.00 0.00 0.00 2.74
1880 5435 7.742963 CGCTCGTTTATATTTGTGTTTTGTAGT 59.257 33.333 0.00 0.00 0.00 2.73
1883 5438 8.505625 TCGTTTATATTTGTGTTTTGTAGTCCC 58.494 33.333 0.00 0.00 0.00 4.46
1899 7024 1.037030 TCCCAATCGATGCAAAGGCC 61.037 55.000 0.00 0.00 40.13 5.19
1950 7075 6.279123 GGTTTTGGTCCGTTGGTAAAATTTA 58.721 36.000 0.00 0.00 0.00 1.40
2016 7227 9.230932 CTTTTTGAGAAAACTTCATCTTCAGAC 57.769 33.333 0.00 0.00 31.72 3.51
2020 7231 4.752101 AGAAAACTTCATCTTCAGACCACG 59.248 41.667 0.00 0.00 0.00 4.94
2025 7236 1.132453 TCATCTTCAGACCACGTAGCG 59.868 52.381 0.00 0.00 0.00 4.26
2027 7238 0.520404 TCTTCAGACCACGTAGCGAC 59.480 55.000 0.00 0.00 0.00 5.19
2041 7252 4.289529 GTAGCGACGAAAACAAGTACTG 57.710 45.455 0.00 0.00 0.00 2.74
2042 7253 3.088194 AGCGACGAAAACAAGTACTGA 57.912 42.857 0.00 0.00 0.00 3.41
2043 7254 3.450578 AGCGACGAAAACAAGTACTGAA 58.549 40.909 0.00 0.00 0.00 3.02
2044 7255 3.489785 AGCGACGAAAACAAGTACTGAAG 59.510 43.478 0.00 0.00 0.00 3.02
2045 7256 3.244579 GCGACGAAAACAAGTACTGAAGT 59.755 43.478 0.00 0.00 0.00 3.01
2046 7257 4.605573 GCGACGAAAACAAGTACTGAAGTC 60.606 45.833 0.00 0.00 0.00 3.01
2047 7258 4.738740 CGACGAAAACAAGTACTGAAGTCT 59.261 41.667 0.00 0.00 0.00 3.24
2048 7259 5.231568 CGACGAAAACAAGTACTGAAGTCTT 59.768 40.000 0.00 0.00 0.00 3.01
2049 7260 6.237755 CGACGAAAACAAGTACTGAAGTCTTT 60.238 38.462 0.00 0.82 0.00 2.52
2050 7261 7.373778 ACGAAAACAAGTACTGAAGTCTTTT 57.626 32.000 0.00 0.00 0.00 2.27
2051 7262 7.241376 ACGAAAACAAGTACTGAAGTCTTTTG 58.759 34.615 0.00 6.48 0.00 2.44
2052 7263 7.118680 ACGAAAACAAGTACTGAAGTCTTTTGA 59.881 33.333 0.00 0.00 0.00 2.69
2071 7282 9.465985 TCTTTTGACCATTTAATAACGAAAACC 57.534 29.630 0.00 0.00 0.00 3.27
2072 7283 9.250624 CTTTTGACCATTTAATAACGAAAACCA 57.749 29.630 0.00 0.00 0.00 3.67
2073 7284 8.804688 TTTGACCATTTAATAACGAAAACCAG 57.195 30.769 0.00 0.00 0.00 4.00
2074 7285 7.513371 TGACCATTTAATAACGAAAACCAGT 57.487 32.000 0.00 0.00 0.00 4.00
2093 7304 0.170561 TACTGAAGCGAGACGAAGGC 59.829 55.000 0.00 0.00 0.00 4.35
2094 7305 1.080501 CTGAAGCGAGACGAAGGCA 60.081 57.895 0.00 0.00 0.00 4.75
2116 7327 2.514824 GCTGTCATCGCCCCTTCC 60.515 66.667 0.00 0.00 0.00 3.46
2118 7329 1.153289 CTGTCATCGCCCCTTCCTG 60.153 63.158 0.00 0.00 0.00 3.86
2119 7330 2.514824 GTCATCGCCCCTTCCTGC 60.515 66.667 0.00 0.00 0.00 4.85
2120 7331 2.688666 TCATCGCCCCTTCCTGCT 60.689 61.111 0.00 0.00 0.00 4.24
2126 7337 4.479993 CCCCTTCCTGCTCGCCAG 62.480 72.222 0.00 0.00 41.41 4.85
2127 7338 3.393970 CCCTTCCTGCTCGCCAGA 61.394 66.667 4.72 0.00 44.64 3.86
2140 7352 1.202710 TCGCCAGAGCCACAAAAGTTA 60.203 47.619 0.00 0.00 34.57 2.24
2143 7355 3.438781 CGCCAGAGCCACAAAAGTTATTA 59.561 43.478 0.00 0.00 34.57 0.98
2166 7378 8.922058 TTATATTAAACAGTCTGGAAGTCGTC 57.078 34.615 4.53 0.00 33.76 4.20
2168 7380 6.585695 ATTAAACAGTCTGGAAGTCGTCTA 57.414 37.500 4.53 0.00 33.76 2.59
2172 7384 4.618965 ACAGTCTGGAAGTCGTCTAAAAC 58.381 43.478 4.53 0.00 33.76 2.43
2173 7385 3.988517 CAGTCTGGAAGTCGTCTAAAACC 59.011 47.826 0.00 0.00 33.76 3.27
2176 7388 2.038033 CTGGAAGTCGTCTAAAACCCCA 59.962 50.000 0.00 0.00 0.00 4.96
2178 7390 3.839490 TGGAAGTCGTCTAAAACCCCATA 59.161 43.478 0.00 0.00 0.00 2.74
2179 7391 4.286549 TGGAAGTCGTCTAAAACCCCATAA 59.713 41.667 0.00 0.00 0.00 1.90
2180 7392 4.874396 GGAAGTCGTCTAAAACCCCATAAG 59.126 45.833 0.00 0.00 0.00 1.73
2181 7393 5.337813 GGAAGTCGTCTAAAACCCCATAAGA 60.338 44.000 0.00 0.00 0.00 2.10
2183 7395 4.081254 AGTCGTCTAAAACCCCATAAGACC 60.081 45.833 0.00 0.00 34.42 3.85
2185 7397 4.286549 TCGTCTAAAACCCCATAAGACCAA 59.713 41.667 0.00 0.00 34.42 3.67
2186 7398 5.045432 TCGTCTAAAACCCCATAAGACCAAT 60.045 40.000 0.00 0.00 34.42 3.16
2187 7399 5.065988 CGTCTAAAACCCCATAAGACCAATG 59.934 44.000 0.00 0.00 34.42 2.82
2188 7400 4.953579 TCTAAAACCCCATAAGACCAATGC 59.046 41.667 0.00 0.00 0.00 3.56
2189 7401 2.917713 AACCCCATAAGACCAATGCA 57.082 45.000 0.00 0.00 0.00 3.96
2190 7402 2.143876 ACCCCATAAGACCAATGCAC 57.856 50.000 0.00 0.00 0.00 4.57
2191 7403 1.341976 ACCCCATAAGACCAATGCACC 60.342 52.381 0.00 0.00 0.00 5.01
2192 7404 1.341877 CCCCATAAGACCAATGCACCA 60.342 52.381 0.00 0.00 0.00 4.17
2196 7408 3.129287 CCATAAGACCAATGCACCAGAAC 59.871 47.826 0.00 0.00 0.00 3.01
2203 7415 2.101249 CCAATGCACCAGAACAACAACT 59.899 45.455 0.00 0.00 0.00 3.16
2205 7417 0.455410 TGCACCAGAACAACAACTGC 59.545 50.000 0.00 0.00 33.40 4.40
2225 7437 0.525668 CGCCGATGAAGAGTAGCGTT 60.526 55.000 0.00 0.00 38.81 4.84
2231 7443 3.546218 CGATGAAGAGTAGCGTTGATCGA 60.546 47.826 0.00 0.00 42.86 3.59
2259 7471 2.234300 ACCTGAAAACACACGATCGT 57.766 45.000 16.60 16.60 0.00 3.73
2274 7497 3.550992 CGTGACGAAATCCGCCGG 61.551 66.667 0.00 0.00 43.32 6.13
2285 7508 4.436998 CCGCCGGAGACACACCTC 62.437 72.222 5.05 0.00 0.00 3.85
2293 7516 2.088674 GAGACACACCTCCACACGCT 62.089 60.000 0.00 0.00 0.00 5.07
2296 7519 1.956170 CACACCTCCACACGCTCAC 60.956 63.158 0.00 0.00 0.00 3.51
2298 7521 3.991051 ACCTCCACACGCTCACCG 61.991 66.667 0.00 0.00 44.21 4.94
2317 7540 2.224137 CCGATGATGCTAGACACACCAT 60.224 50.000 0.00 0.00 0.00 3.55
2323 7546 3.610040 TGCTAGACACACCATCGAAAT 57.390 42.857 0.00 0.00 0.00 2.17
2328 7551 1.398390 GACACACCATCGAAATGAGGC 59.602 52.381 0.00 0.00 34.61 4.70
2329 7552 1.003580 ACACACCATCGAAATGAGGCT 59.996 47.619 0.00 0.00 34.61 4.58
2330 7553 2.236146 ACACACCATCGAAATGAGGCTA 59.764 45.455 0.00 0.00 34.61 3.93
2331 7554 2.609459 CACACCATCGAAATGAGGCTAC 59.391 50.000 0.00 0.00 34.61 3.58
2332 7555 2.236146 ACACCATCGAAATGAGGCTACA 59.764 45.455 0.00 0.00 34.61 2.74
2333 7556 2.609459 CACCATCGAAATGAGGCTACAC 59.391 50.000 0.00 0.00 34.61 2.90
2334 7557 1.860950 CCATCGAAATGAGGCTACACG 59.139 52.381 0.00 0.00 34.61 4.49
2335 7558 1.860950 CATCGAAATGAGGCTACACGG 59.139 52.381 0.00 0.00 34.61 4.94
2336 7559 0.174845 TCGAAATGAGGCTACACGGG 59.825 55.000 0.00 0.00 0.00 5.28
2337 7560 0.810031 CGAAATGAGGCTACACGGGG 60.810 60.000 0.00 0.00 0.00 5.73
2338 7561 0.539986 GAAATGAGGCTACACGGGGA 59.460 55.000 0.00 0.00 0.00 4.81
2339 7562 0.541863 AAATGAGGCTACACGGGGAG 59.458 55.000 0.00 0.00 0.00 4.30
2340 7563 0.325296 AATGAGGCTACACGGGGAGA 60.325 55.000 0.00 0.00 0.00 3.71
2341 7564 1.043673 ATGAGGCTACACGGGGAGAC 61.044 60.000 0.00 0.00 0.00 3.36
2342 7565 1.681327 GAGGCTACACGGGGAGACA 60.681 63.158 4.96 0.00 0.00 3.41
2343 7566 1.946475 GAGGCTACACGGGGAGACAC 61.946 65.000 4.96 0.00 0.00 3.67
2344 7567 2.280552 GGCTACACGGGGAGACACA 61.281 63.158 0.00 0.00 0.00 3.72
2345 7568 1.080025 GCTACACGGGGAGACACAC 60.080 63.158 0.00 0.00 0.00 3.82
2346 7569 1.590147 CTACACGGGGAGACACACC 59.410 63.158 0.00 0.00 39.03 4.16
2347 7570 0.898789 CTACACGGGGAGACACACCT 60.899 60.000 0.00 0.00 40.56 4.00
2348 7571 0.896940 TACACGGGGAGACACACCTC 60.897 60.000 0.00 0.00 40.56 3.85
2354 7577 4.655527 GAGACACACCTCCACACG 57.344 61.111 0.00 0.00 0.00 4.49
2355 7578 1.664965 GAGACACACCTCCACACGC 60.665 63.158 0.00 0.00 0.00 5.34
2356 7579 2.088674 GAGACACACCTCCACACGCT 62.089 60.000 0.00 0.00 0.00 5.07
2357 7580 1.664965 GACACACCTCCACACGCTC 60.665 63.158 0.00 0.00 0.00 5.03
2358 7581 2.363711 GACACACCTCCACACGCTCA 62.364 60.000 0.00 0.00 0.00 4.26
2359 7582 1.956170 CACACCTCCACACGCTCAC 60.956 63.158 0.00 0.00 0.00 3.51
2360 7583 2.357517 CACCTCCACACGCTCACC 60.358 66.667 0.00 0.00 0.00 4.02
2361 7584 3.991051 ACCTCCACACGCTCACCG 61.991 66.667 0.00 0.00 44.21 4.94
2362 7585 3.680786 CCTCCACACGCTCACCGA 61.681 66.667 0.00 0.00 41.02 4.69
2363 7586 2.573869 CTCCACACGCTCACCGAT 59.426 61.111 0.00 0.00 41.02 4.18
2364 7587 1.807165 CTCCACACGCTCACCGATG 60.807 63.158 0.00 0.00 41.02 3.84
2365 7588 2.212900 CTCCACACGCTCACCGATGA 62.213 60.000 0.00 0.00 41.02 2.92
2366 7589 1.153568 CCACACGCTCACCGATGAT 60.154 57.895 0.00 0.00 41.02 2.45
2367 7590 0.102300 CCACACGCTCACCGATGATA 59.898 55.000 0.00 0.00 41.02 2.15
2368 7591 1.200483 CACACGCTCACCGATGATAC 58.800 55.000 0.00 0.00 41.02 2.24
2369 7592 1.103803 ACACGCTCACCGATGATACT 58.896 50.000 0.00 0.00 41.02 2.12
2370 7593 2.032924 CACACGCTCACCGATGATACTA 59.967 50.000 0.00 0.00 41.02 1.82
2371 7594 2.290916 ACACGCTCACCGATGATACTAG 59.709 50.000 0.00 0.00 41.02 2.57
2372 7595 2.548480 CACGCTCACCGATGATACTAGA 59.452 50.000 0.00 0.00 41.02 2.43
2373 7596 2.548904 ACGCTCACCGATGATACTAGAC 59.451 50.000 0.00 0.00 41.02 2.59
2374 7597 2.548480 CGCTCACCGATGATACTAGACA 59.452 50.000 0.00 0.00 40.02 3.41
2375 7598 3.607310 CGCTCACCGATGATACTAGACAC 60.607 52.174 0.00 0.00 40.02 3.67
2376 7599 3.315470 GCTCACCGATGATACTAGACACA 59.685 47.826 0.00 0.00 33.22 3.72
2377 7600 4.790123 GCTCACCGATGATACTAGACACAC 60.790 50.000 0.00 0.00 33.22 3.82
2378 7601 3.630769 TCACCGATGATACTAGACACACC 59.369 47.826 0.00 0.00 0.00 4.16
2379 7602 3.380320 CACCGATGATACTAGACACACCA 59.620 47.826 0.00 0.00 0.00 4.17
2380 7603 4.038042 CACCGATGATACTAGACACACCAT 59.962 45.833 0.00 0.00 0.00 3.55
2381 7604 4.278669 ACCGATGATACTAGACACACCATC 59.721 45.833 0.00 0.00 0.00 3.51
2382 7605 4.278419 CCGATGATACTAGACACACCATCA 59.722 45.833 0.00 0.00 31.85 3.07
2383 7606 5.221244 CCGATGATACTAGACACACCATCAA 60.221 44.000 0.00 0.00 31.85 2.57
2384 7607 6.273071 CGATGATACTAGACACACCATCAAA 58.727 40.000 0.00 0.00 31.85 2.69
2385 7608 6.756542 CGATGATACTAGACACACCATCAAAA 59.243 38.462 0.00 0.00 31.85 2.44
2386 7609 7.254117 CGATGATACTAGACACACCATCAAAAC 60.254 40.741 0.00 0.00 31.85 2.43
2387 7610 5.867174 TGATACTAGACACACCATCAAAACG 59.133 40.000 0.00 0.00 0.00 3.60
2388 7611 4.330944 ACTAGACACACCATCAAAACGA 57.669 40.909 0.00 0.00 0.00 3.85
2389 7612 4.307432 ACTAGACACACCATCAAAACGAG 58.693 43.478 0.00 0.00 0.00 4.18
2398 7621 1.082117 ATCAAAACGAGGCTACGCGG 61.082 55.000 12.47 0.00 44.51 6.46
2405 7628 3.427598 GAGGCTACGCGGGGAGAAC 62.428 68.421 17.25 7.32 0.00 3.01
2406 7629 4.867599 GGCTACGCGGGGAGAACG 62.868 72.222 17.25 0.00 0.00 3.95
2407 7630 4.125695 GCTACGCGGGGAGAACGT 62.126 66.667 17.25 1.05 43.45 3.99
2410 7633 0.383231 CTACGCGGGGAGAACGTTAT 59.617 55.000 12.47 0.00 40.99 1.89
2411 7634 0.381801 TACGCGGGGAGAACGTTATC 59.618 55.000 14.46 14.46 40.99 1.75
2413 7636 0.594284 CGCGGGGAGAACGTTATCTC 60.594 60.000 21.18 18.04 44.18 2.75
2414 7637 0.458669 GCGGGGAGAACGTTATCTCA 59.541 55.000 23.22 0.00 46.24 3.27
2420 7643 4.811557 GGGGAGAACGTTATCTCATTTCAG 59.188 45.833 23.22 0.00 46.24 3.02
2424 7647 5.665459 AGAACGTTATCTCATTTCAGGGAG 58.335 41.667 0.00 0.00 0.00 4.30
2444 7667 1.154654 CGCCGCTGTCTCGTTTTTC 60.155 57.895 0.00 0.00 0.00 2.29
2446 7669 1.425412 GCCGCTGTCTCGTTTTTCTA 58.575 50.000 0.00 0.00 0.00 2.10
2451 7674 3.918591 CGCTGTCTCGTTTTTCTAAGCTA 59.081 43.478 0.00 0.00 0.00 3.32
2462 7685 6.436261 GTTTTTCTAAGCTAGACACAAACCC 58.564 40.000 0.00 0.00 33.84 4.11
2469 7692 5.043737 AGCTAGACACAAACCCTAACAAA 57.956 39.130 0.00 0.00 0.00 2.83
2474 7697 7.012610 GCTAGACACAAACCCTAACAAAACTTA 59.987 37.037 0.00 0.00 0.00 2.24
2477 7700 8.586744 AGACACAAACCCTAACAAAACTTAAAA 58.413 29.630 0.00 0.00 0.00 1.52
2505 7728 8.753497 ATATCTAAAAATGAAGTCCTTCCACC 57.247 34.615 4.67 0.00 38.77 4.61
2524 7747 3.512516 GCAAGCGCTGGGATCCAC 61.513 66.667 12.58 3.53 34.30 4.02
2543 7766 1.747367 CGCGCCCCATGGACTTAAA 60.747 57.895 15.22 0.00 0.00 1.52
2549 7772 0.395173 CCCATGGACTTAAACCCCCG 60.395 60.000 15.22 0.00 0.00 5.73
2597 7820 1.011595 AGAGAGGCAGAGGAACCCTA 58.988 55.000 0.00 0.00 31.76 3.53
2603 7826 2.250273 AGGCAGAGGAACCCTAATAGGA 59.750 50.000 8.12 0.00 37.67 2.94
2609 7832 5.071115 CAGAGGAACCCTAATAGGAAGAAGG 59.929 48.000 8.12 0.00 37.67 3.46
2616 7839 0.464554 AATAGGAAGAAGGCGGCTGC 60.465 55.000 14.21 11.76 41.71 5.25
2617 7840 1.626356 ATAGGAAGAAGGCGGCTGCA 61.626 55.000 20.75 0.00 45.35 4.41
2638 7861 7.440556 GCTGCATAAGAGATCATGTCTTCTAAA 59.559 37.037 0.00 0.00 37.29 1.85
2641 7864 8.763356 GCATAAGAGATCATGTCTTCTAAACAG 58.237 37.037 0.00 0.00 37.29 3.16
2650 7873 9.768662 ATCATGTCTTCTAAACAGCAAATTTTT 57.231 25.926 0.00 0.00 0.00 1.94
2793 8017 7.581213 TTTGATTCTTTGTAGGCAAAAGAGA 57.419 32.000 9.14 3.85 43.17 3.10
2809 8033 1.983119 GAGATCCGGATTGGGTGGCA 61.983 60.000 20.22 0.00 38.76 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.706190 AGCCCCACATGTCTTATACTCC 59.294 50.000 0.00 0.00 0.00 3.85
3 4 7.425606 CAATTTAAGCCCCACATGTCTTATAC 58.574 38.462 0.00 0.00 0.00 1.47
4 5 6.549364 CCAATTTAAGCCCCACATGTCTTATA 59.451 38.462 0.00 0.00 0.00 0.98
6 7 4.709397 CCAATTTAAGCCCCACATGTCTTA 59.291 41.667 0.00 0.00 0.00 2.10
9 10 2.418609 GCCAATTTAAGCCCCACATGTC 60.419 50.000 0.00 0.00 0.00 3.06
160 165 3.861276 AGATGTGTGCATGTTTGGATG 57.139 42.857 0.00 0.00 35.07 3.51
225 230 9.013490 GCAGCACATGTGTATTTTTCTATTAAG 57.987 33.333 26.01 3.17 0.00 1.85
296 301 6.472016 TGCTACACCATTCAGTCTTCATAAA 58.528 36.000 0.00 0.00 0.00 1.40
299 304 4.511527 CTGCTACACCATTCAGTCTTCAT 58.488 43.478 0.00 0.00 0.00 2.57
343 348 3.391631 CGTCTTGAACGCGCGACA 61.392 61.111 39.36 30.18 45.76 4.35
463 471 0.840617 TTTTCCCACAAAAAGGCCCC 59.159 50.000 0.00 0.00 0.00 5.80
552 562 0.612732 CAACATGCCATGGGTCCTGT 60.613 55.000 15.13 4.18 33.60 4.00
554 564 1.000739 CCAACATGCCATGGGTCCT 59.999 57.895 15.13 0.00 32.87 3.85
591 601 4.063967 CTCCGCTGTGTACGCCCA 62.064 66.667 3.51 0.00 0.00 5.36
605 615 1.402325 GCAAATACGGTGCAAACCTCC 60.402 52.381 0.00 0.00 41.80 4.30
606 616 1.977188 GCAAATACGGTGCAAACCTC 58.023 50.000 0.00 0.00 41.80 3.85
639 649 5.856455 GCATACATTGAACTGGTGTAACAAC 59.144 40.000 0.00 0.00 39.98 3.32
655 665 4.588899 TGCTAGAACTTGTGGCATACATT 58.411 39.130 0.00 0.00 39.48 2.71
683 693 2.805671 TGAACTTGACGCAAACGATCAT 59.194 40.909 0.00 0.00 43.93 2.45
732 742 9.454859 GCCTATTATCCAGTTAGCTGAAAATAT 57.545 33.333 8.34 0.00 45.28 1.28
742 752 3.673594 CGGAGCGCCTATTATCCAGTTAG 60.674 52.174 2.29 0.00 0.00 2.34
764 774 7.118680 TGGTACGTGGAAAATCTGTCTTTTATC 59.881 37.037 0.00 0.00 0.00 1.75
765 775 6.938030 TGGTACGTGGAAAATCTGTCTTTTAT 59.062 34.615 0.00 0.00 0.00 1.40
768 778 4.514066 GTGGTACGTGGAAAATCTGTCTTT 59.486 41.667 0.00 0.00 0.00 2.52
842 853 2.158652 AGGGCATGACTCATCTCCATTG 60.159 50.000 0.00 0.00 0.00 2.82
844 855 1.817087 AGGGCATGACTCATCTCCAT 58.183 50.000 0.00 0.83 0.00 3.41
845 856 1.487976 GAAGGGCATGACTCATCTCCA 59.512 52.381 0.00 0.00 0.00 3.86
848 859 1.411977 CTCGAAGGGCATGACTCATCT 59.588 52.381 0.00 0.00 0.00 2.90
849 860 1.410517 TCTCGAAGGGCATGACTCATC 59.589 52.381 0.00 0.00 0.00 2.92
906 917 2.415357 CCGCGAATAAACAAAGCCACAT 60.415 45.455 8.23 0.00 0.00 3.21
1061 4598 2.551887 TGTGTGATGTGTATGGTTGTGC 59.448 45.455 0.00 0.00 0.00 4.57
1071 4608 2.936919 ACAGGTGATGTGTGATGTGT 57.063 45.000 0.00 0.00 41.91 3.72
1072 4609 4.192429 TCTACAGGTGATGTGTGATGTG 57.808 45.455 0.00 0.00 43.80 3.21
1073 4610 4.440663 CGATCTACAGGTGATGTGTGATGT 60.441 45.833 0.00 0.00 43.80 3.06
1074 4611 4.047142 CGATCTACAGGTGATGTGTGATG 58.953 47.826 0.00 0.00 43.80 3.07
1075 4612 3.954258 TCGATCTACAGGTGATGTGTGAT 59.046 43.478 0.00 0.00 43.80 3.06
1076 4613 3.128764 GTCGATCTACAGGTGATGTGTGA 59.871 47.826 0.00 0.00 43.80 3.58
1077 4614 3.439293 GTCGATCTACAGGTGATGTGTG 58.561 50.000 0.00 0.00 43.80 3.82
1112 4649 1.421410 CTGGTACTCCATTGTCGCGC 61.421 60.000 0.00 0.00 43.43 6.86
1332 4869 0.397941 CAGGCAGGTCTGTCCTTGAA 59.602 55.000 9.96 0.00 45.67 2.69
1364 4901 1.087501 TGACCGATCGAGTGAGTCTG 58.912 55.000 18.66 0.00 0.00 3.51
1365 4902 1.944024 GATGACCGATCGAGTGAGTCT 59.056 52.381 18.66 5.10 0.00 3.24
1673 5216 0.464373 AACACAGACACAGCACAGGG 60.464 55.000 0.00 0.00 0.00 4.45
1733 5283 2.417586 GGCGCCCATTATTTATCCGTAC 59.582 50.000 18.11 0.00 0.00 3.67
1824 5379 2.420022 CGATGGGGTTTTAGCACTTCAG 59.580 50.000 0.00 0.00 0.00 3.02
1825 5380 2.224670 ACGATGGGGTTTTAGCACTTCA 60.225 45.455 0.00 0.00 0.00 3.02
1826 5381 2.433436 ACGATGGGGTTTTAGCACTTC 58.567 47.619 0.00 0.00 0.00 3.01
1827 5382 2.579410 ACGATGGGGTTTTAGCACTT 57.421 45.000 0.00 0.00 0.00 3.16
1828 5383 3.706600 TTACGATGGGGTTTTAGCACT 57.293 42.857 0.00 0.00 0.00 4.40
1829 5384 6.439675 TTTATTACGATGGGGTTTTAGCAC 57.560 37.500 0.00 0.00 0.00 4.40
1830 5385 5.066764 GCTTTATTACGATGGGGTTTTAGCA 59.933 40.000 0.00 0.00 0.00 3.49
1831 5386 5.516996 GCTTTATTACGATGGGGTTTTAGC 58.483 41.667 0.00 0.00 0.00 3.09
1832 5387 5.744490 CGCTTTATTACGATGGGGTTTTAG 58.256 41.667 0.00 0.00 0.00 1.85
1833 5388 4.035441 GCGCTTTATTACGATGGGGTTTTA 59.965 41.667 0.00 0.00 0.00 1.52
1834 5389 3.181494 GCGCTTTATTACGATGGGGTTTT 60.181 43.478 0.00 0.00 0.00 2.43
1835 5390 2.356695 GCGCTTTATTACGATGGGGTTT 59.643 45.455 0.00 0.00 0.00 3.27
1836 5391 1.944709 GCGCTTTATTACGATGGGGTT 59.055 47.619 0.00 0.00 0.00 4.11
1837 5392 1.140252 AGCGCTTTATTACGATGGGGT 59.860 47.619 2.64 0.00 0.00 4.95
1838 5393 1.798813 GAGCGCTTTATTACGATGGGG 59.201 52.381 13.26 0.00 0.00 4.96
1839 5394 1.455786 CGAGCGCTTTATTACGATGGG 59.544 52.381 13.26 0.00 0.00 4.00
1877 5432 2.917933 CCTTTGCATCGATTGGGACTA 58.082 47.619 0.00 0.00 0.00 2.59
1878 5433 1.755179 CCTTTGCATCGATTGGGACT 58.245 50.000 0.00 0.00 0.00 3.85
1879 5434 0.101219 GCCTTTGCATCGATTGGGAC 59.899 55.000 0.00 0.00 37.47 4.46
1880 5435 1.037030 GGCCTTTGCATCGATTGGGA 61.037 55.000 0.00 0.00 40.13 4.37
1883 5438 2.198406 CATTGGCCTTTGCATCGATTG 58.802 47.619 3.32 0.00 40.13 2.67
1899 7024 5.524511 TCGACCGATTGAAGTTTACATTG 57.475 39.130 0.00 0.00 0.00 2.82
1998 7155 4.511826 ACGTGGTCTGAAGATGAAGTTTTC 59.488 41.667 0.00 0.00 0.00 2.29
1999 7156 4.451900 ACGTGGTCTGAAGATGAAGTTTT 58.548 39.130 0.00 0.00 0.00 2.43
2003 7160 3.182967 GCTACGTGGTCTGAAGATGAAG 58.817 50.000 0.00 0.00 0.00 3.02
2004 7161 2.415491 CGCTACGTGGTCTGAAGATGAA 60.415 50.000 0.00 0.00 0.00 2.57
2009 7220 0.793478 CGTCGCTACGTGGTCTGAAG 60.793 60.000 2.05 0.00 44.21 3.02
2020 7231 3.976942 TCAGTACTTGTTTTCGTCGCTAC 59.023 43.478 0.00 0.00 0.00 3.58
2025 7236 6.585389 AAGACTTCAGTACTTGTTTTCGTC 57.415 37.500 0.00 0.00 0.00 4.20
2027 7238 7.425595 GTCAAAAGACTTCAGTACTTGTTTTCG 59.574 37.037 0.00 0.00 0.00 3.46
2030 7241 6.657541 TGGTCAAAAGACTTCAGTACTTGTTT 59.342 34.615 0.00 0.00 0.00 2.83
2031 7242 6.177610 TGGTCAAAAGACTTCAGTACTTGTT 58.822 36.000 0.00 0.00 0.00 2.83
2039 7250 9.329913 CGTTATTAAATGGTCAAAAGACTTCAG 57.670 33.333 0.00 0.00 0.00 3.02
2040 7251 9.058174 TCGTTATTAAATGGTCAAAAGACTTCA 57.942 29.630 0.00 0.00 0.00 3.02
2041 7252 9.887406 TTCGTTATTAAATGGTCAAAAGACTTC 57.113 29.630 0.00 0.00 0.00 3.01
2045 7256 9.465985 GGTTTTCGTTATTAAATGGTCAAAAGA 57.534 29.630 0.00 0.00 0.00 2.52
2046 7257 9.250624 TGGTTTTCGTTATTAAATGGTCAAAAG 57.749 29.630 0.00 0.00 0.00 2.27
2047 7258 9.250624 CTGGTTTTCGTTATTAAATGGTCAAAA 57.749 29.630 0.00 0.00 0.00 2.44
2048 7259 8.414778 ACTGGTTTTCGTTATTAAATGGTCAAA 58.585 29.630 0.00 0.00 0.00 2.69
2049 7260 7.942990 ACTGGTTTTCGTTATTAAATGGTCAA 58.057 30.769 0.00 0.00 0.00 3.18
2050 7261 7.513371 ACTGGTTTTCGTTATTAAATGGTCA 57.487 32.000 0.00 0.00 0.00 4.02
2051 7262 8.724229 AGTACTGGTTTTCGTTATTAAATGGTC 58.276 33.333 0.00 0.00 0.00 4.02
2052 7263 8.508875 CAGTACTGGTTTTCGTTATTAAATGGT 58.491 33.333 15.49 0.00 0.00 3.55
2053 7264 8.723311 TCAGTACTGGTTTTCGTTATTAAATGG 58.277 33.333 22.48 0.00 0.00 3.16
2056 7267 8.284693 GCTTCAGTACTGGTTTTCGTTATTAAA 58.715 33.333 22.48 3.66 0.00 1.52
2057 7268 7.359431 CGCTTCAGTACTGGTTTTCGTTATTAA 60.359 37.037 22.48 4.08 0.00 1.40
2058 7269 6.089820 CGCTTCAGTACTGGTTTTCGTTATTA 59.910 38.462 22.48 0.00 0.00 0.98
2059 7270 5.107220 CGCTTCAGTACTGGTTTTCGTTATT 60.107 40.000 22.48 0.00 0.00 1.40
2060 7271 4.387862 CGCTTCAGTACTGGTTTTCGTTAT 59.612 41.667 22.48 0.00 0.00 1.89
2061 7272 3.737266 CGCTTCAGTACTGGTTTTCGTTA 59.263 43.478 22.48 0.00 0.00 3.18
2062 7273 2.542595 CGCTTCAGTACTGGTTTTCGTT 59.457 45.455 22.48 0.00 0.00 3.85
2063 7274 2.132762 CGCTTCAGTACTGGTTTTCGT 58.867 47.619 22.48 0.00 0.00 3.85
2064 7275 2.400399 TCGCTTCAGTACTGGTTTTCG 58.600 47.619 22.48 17.10 0.00 3.46
2065 7276 3.429207 GTCTCGCTTCAGTACTGGTTTTC 59.571 47.826 22.48 7.14 0.00 2.29
2066 7277 3.391049 GTCTCGCTTCAGTACTGGTTTT 58.609 45.455 22.48 0.00 0.00 2.43
2067 7278 2.607282 CGTCTCGCTTCAGTACTGGTTT 60.607 50.000 22.48 0.00 0.00 3.27
2068 7279 1.068472 CGTCTCGCTTCAGTACTGGTT 60.068 52.381 22.48 0.00 0.00 3.67
2069 7280 0.522180 CGTCTCGCTTCAGTACTGGT 59.478 55.000 22.48 0.00 0.00 4.00
2070 7281 0.803117 TCGTCTCGCTTCAGTACTGG 59.197 55.000 22.48 8.81 0.00 4.00
2071 7282 2.510874 CTTCGTCTCGCTTCAGTACTG 58.489 52.381 17.17 17.17 0.00 2.74
2072 7283 1.469308 CCTTCGTCTCGCTTCAGTACT 59.531 52.381 0.00 0.00 0.00 2.73
2073 7284 1.897641 CCTTCGTCTCGCTTCAGTAC 58.102 55.000 0.00 0.00 0.00 2.73
2074 7285 0.170561 GCCTTCGTCTCGCTTCAGTA 59.829 55.000 0.00 0.00 0.00 2.74
2098 7309 2.892425 GAAGGGGCGATGACAGCG 60.892 66.667 9.11 9.11 35.00 5.18
2099 7310 2.514824 GGAAGGGGCGATGACAGC 60.515 66.667 0.00 0.00 0.00 4.40
2101 7312 2.989639 CAGGAAGGGGCGATGACA 59.010 61.111 0.00 0.00 0.00 3.58
2119 7330 0.886490 ACTTTTGTGGCTCTGGCGAG 60.886 55.000 0.00 0.00 39.81 5.03
2120 7331 0.465460 AACTTTTGTGGCTCTGGCGA 60.465 50.000 0.00 0.00 39.81 5.54
2140 7352 9.530633 GACGACTTCCAGACTGTTTAATATAAT 57.469 33.333 0.93 0.00 0.00 1.28
2143 7355 7.171630 AGACGACTTCCAGACTGTTTAATAT 57.828 36.000 0.93 0.00 0.00 1.28
2149 7361 4.931661 TTTAGACGACTTCCAGACTGTT 57.068 40.909 0.93 0.00 0.00 3.16
2153 7365 3.324117 GGGTTTTAGACGACTTCCAGAC 58.676 50.000 0.00 0.00 0.00 3.51
2156 7368 2.048601 TGGGGTTTTAGACGACTTCCA 58.951 47.619 0.00 0.00 0.00 3.53
2164 7376 5.163550 GCATTGGTCTTATGGGGTTTTAGAC 60.164 44.000 0.00 0.00 35.61 2.59
2165 7377 4.953579 GCATTGGTCTTATGGGGTTTTAGA 59.046 41.667 0.00 0.00 0.00 2.10
2166 7378 4.709397 TGCATTGGTCTTATGGGGTTTTAG 59.291 41.667 0.00 0.00 0.00 1.85
2168 7380 3.260632 GTGCATTGGTCTTATGGGGTTTT 59.739 43.478 0.00 0.00 0.00 2.43
2172 7384 1.341877 TGGTGCATTGGTCTTATGGGG 60.342 52.381 0.00 0.00 0.00 4.96
2173 7385 2.026641 CTGGTGCATTGGTCTTATGGG 58.973 52.381 0.00 0.00 0.00 4.00
2176 7388 4.032960 TGTTCTGGTGCATTGGTCTTAT 57.967 40.909 0.00 0.00 0.00 1.73
2178 7390 2.362077 GTTGTTCTGGTGCATTGGTCTT 59.638 45.455 0.00 0.00 0.00 3.01
2179 7391 1.956477 GTTGTTCTGGTGCATTGGTCT 59.044 47.619 0.00 0.00 0.00 3.85
2180 7392 1.680735 TGTTGTTCTGGTGCATTGGTC 59.319 47.619 0.00 0.00 0.00 4.02
2181 7393 1.774110 TGTTGTTCTGGTGCATTGGT 58.226 45.000 0.00 0.00 0.00 3.67
2183 7395 3.117794 CAGTTGTTGTTCTGGTGCATTG 58.882 45.455 0.00 0.00 0.00 2.82
2185 7397 1.067516 GCAGTTGTTGTTCTGGTGCAT 59.932 47.619 0.00 0.00 32.94 3.96
2186 7398 0.455410 GCAGTTGTTGTTCTGGTGCA 59.545 50.000 0.00 0.00 32.94 4.57
2187 7399 0.249031 GGCAGTTGTTGTTCTGGTGC 60.249 55.000 0.00 0.00 32.94 5.01
2188 7400 0.029300 CGGCAGTTGTTGTTCTGGTG 59.971 55.000 0.00 0.00 32.94 4.17
2189 7401 1.724582 GCGGCAGTTGTTGTTCTGGT 61.725 55.000 0.00 0.00 32.94 4.00
2190 7402 1.008538 GCGGCAGTTGTTGTTCTGG 60.009 57.895 0.00 0.00 32.94 3.86
2191 7403 1.008538 GGCGGCAGTTGTTGTTCTG 60.009 57.895 3.07 0.00 35.12 3.02
2192 7404 2.542907 CGGCGGCAGTTGTTGTTCT 61.543 57.895 10.53 0.00 0.00 3.01
2196 7408 1.851021 TTCATCGGCGGCAGTTGTTG 61.851 55.000 10.53 0.00 0.00 3.33
2203 7415 1.437573 CTACTCTTCATCGGCGGCA 59.562 57.895 10.53 0.00 0.00 5.69
2205 7417 1.658717 CGCTACTCTTCATCGGCGG 60.659 63.158 7.21 0.00 39.12 6.13
2225 7437 4.551702 TTCAGGTTGGATCTTTCGATCA 57.448 40.909 4.89 0.00 46.36 2.92
2231 7443 4.202010 CGTGTGTTTTCAGGTTGGATCTTT 60.202 41.667 0.00 0.00 0.00 2.52
2241 7453 2.096909 GTCACGATCGTGTGTTTTCAGG 60.097 50.000 38.72 16.63 45.55 3.86
2259 7471 2.183300 CTCCGGCGGATTTCGTCA 59.817 61.111 31.23 3.96 44.96 4.35
2260 7472 1.877165 GTCTCCGGCGGATTTCGTC 60.877 63.158 31.23 11.71 41.72 4.20
2263 7486 1.079405 TGTGTCTCCGGCGGATTTC 60.079 57.895 31.23 21.40 0.00 2.17
2274 7497 1.664965 GCGTGTGGAGGTGTGTCTC 60.665 63.158 0.00 0.00 0.00 3.36
2285 7508 1.153568 ATCATCGGTGAGCGTGTGG 60.154 57.895 3.97 0.00 37.87 4.17
2288 7511 0.249031 TAGCATCATCGGTGAGCGTG 60.249 55.000 3.97 0.00 37.87 5.34
2293 7516 2.099405 TGTGTCTAGCATCATCGGTGA 58.901 47.619 0.00 0.00 39.04 4.02
2296 7519 1.136891 TGGTGTGTCTAGCATCATCGG 59.863 52.381 0.00 0.00 0.00 4.18
2317 7540 0.174845 CCCGTGTAGCCTCATTTCGA 59.825 55.000 0.00 0.00 0.00 3.71
2323 7546 1.681327 GTCTCCCCGTGTAGCCTCA 60.681 63.158 0.00 0.00 0.00 3.86
2328 7551 0.898789 AGGTGTGTCTCCCCGTGTAG 60.899 60.000 0.00 0.00 0.00 2.74
2329 7552 0.896940 GAGGTGTGTCTCCCCGTGTA 60.897 60.000 0.00 0.00 0.00 2.90
2330 7553 2.122989 AGGTGTGTCTCCCCGTGT 60.123 61.111 0.00 0.00 0.00 4.49
2331 7554 2.657237 GAGGTGTGTCTCCCCGTG 59.343 66.667 0.00 0.00 0.00 4.94
2332 7555 2.603776 GGAGGTGTGTCTCCCCGT 60.604 66.667 0.00 0.00 45.75 5.28
2337 7560 1.664965 GCGTGTGGAGGTGTGTCTC 60.665 63.158 0.00 0.00 0.00 3.36
2338 7561 2.088674 GAGCGTGTGGAGGTGTGTCT 62.089 60.000 0.00 0.00 0.00 3.41
2339 7562 1.664965 GAGCGTGTGGAGGTGTGTC 60.665 63.158 0.00 0.00 0.00 3.67
2340 7563 2.421739 GAGCGTGTGGAGGTGTGT 59.578 61.111 0.00 0.00 0.00 3.72
2341 7564 1.956170 GTGAGCGTGTGGAGGTGTG 60.956 63.158 0.00 0.00 0.00 3.82
2342 7565 2.421739 GTGAGCGTGTGGAGGTGT 59.578 61.111 0.00 0.00 0.00 4.16
2343 7566 2.357517 GGTGAGCGTGTGGAGGTG 60.358 66.667 0.00 0.00 0.00 4.00
2344 7567 3.991051 CGGTGAGCGTGTGGAGGT 61.991 66.667 0.00 0.00 0.00 3.85
2345 7568 3.006756 ATCGGTGAGCGTGTGGAGG 62.007 63.158 3.30 0.00 0.00 4.30
2346 7569 1.807165 CATCGGTGAGCGTGTGGAG 60.807 63.158 3.30 0.00 0.00 3.86
2347 7570 1.604147 ATCATCGGTGAGCGTGTGGA 61.604 55.000 3.97 0.00 37.87 4.02
2348 7571 0.102300 TATCATCGGTGAGCGTGTGG 59.898 55.000 3.97 0.00 37.87 4.17
2349 7572 1.200483 GTATCATCGGTGAGCGTGTG 58.800 55.000 3.97 4.95 37.87 3.82
2350 7573 1.103803 AGTATCATCGGTGAGCGTGT 58.896 50.000 3.97 0.00 37.87 4.49
2351 7574 2.548480 TCTAGTATCATCGGTGAGCGTG 59.452 50.000 3.97 2.13 37.87 5.34
2352 7575 2.548904 GTCTAGTATCATCGGTGAGCGT 59.451 50.000 3.97 0.00 37.87 5.07
2353 7576 2.548480 TGTCTAGTATCATCGGTGAGCG 59.452 50.000 3.97 0.00 37.87 5.03
2354 7577 3.315470 TGTGTCTAGTATCATCGGTGAGC 59.685 47.826 3.97 0.00 37.87 4.26
2355 7578 4.261238 GGTGTGTCTAGTATCATCGGTGAG 60.261 50.000 3.97 0.00 37.87 3.51
2356 7579 3.630769 GGTGTGTCTAGTATCATCGGTGA 59.369 47.826 0.00 0.00 39.04 4.02
2357 7580 3.380320 TGGTGTGTCTAGTATCATCGGTG 59.620 47.826 0.00 0.00 0.00 4.94
2358 7581 3.628008 TGGTGTGTCTAGTATCATCGGT 58.372 45.455 0.00 0.00 0.00 4.69
2359 7582 4.278419 TGATGGTGTGTCTAGTATCATCGG 59.722 45.833 0.00 0.00 34.13 4.18
2360 7583 5.438761 TGATGGTGTGTCTAGTATCATCG 57.561 43.478 0.00 0.00 34.13 3.84
2361 7584 7.254117 CGTTTTGATGGTGTGTCTAGTATCATC 60.254 40.741 0.00 0.00 0.00 2.92
2362 7585 6.535150 CGTTTTGATGGTGTGTCTAGTATCAT 59.465 38.462 0.00 0.00 0.00 2.45
2363 7586 5.867174 CGTTTTGATGGTGTGTCTAGTATCA 59.133 40.000 0.00 0.00 0.00 2.15
2364 7587 6.097356 TCGTTTTGATGGTGTGTCTAGTATC 58.903 40.000 0.00 0.00 0.00 2.24
2365 7588 6.032956 TCGTTTTGATGGTGTGTCTAGTAT 57.967 37.500 0.00 0.00 0.00 2.12
2366 7589 5.456548 TCGTTTTGATGGTGTGTCTAGTA 57.543 39.130 0.00 0.00 0.00 1.82
2367 7590 4.307432 CTCGTTTTGATGGTGTGTCTAGT 58.693 43.478 0.00 0.00 0.00 2.57
2368 7591 3.679980 CCTCGTTTTGATGGTGTGTCTAG 59.320 47.826 0.00 0.00 0.00 2.43
2369 7592 3.659786 CCTCGTTTTGATGGTGTGTCTA 58.340 45.455 0.00 0.00 0.00 2.59
2370 7593 2.494059 CCTCGTTTTGATGGTGTGTCT 58.506 47.619 0.00 0.00 0.00 3.41
2371 7594 1.069227 GCCTCGTTTTGATGGTGTGTC 60.069 52.381 0.00 0.00 0.00 3.67
2372 7595 0.951558 GCCTCGTTTTGATGGTGTGT 59.048 50.000 0.00 0.00 0.00 3.72
2373 7596 1.238439 AGCCTCGTTTTGATGGTGTG 58.762 50.000 0.00 0.00 0.00 3.82
2374 7597 2.423577 GTAGCCTCGTTTTGATGGTGT 58.576 47.619 0.00 0.00 0.00 4.16
2375 7598 1.393539 CGTAGCCTCGTTTTGATGGTG 59.606 52.381 0.00 0.00 0.00 4.17
2376 7599 1.722011 CGTAGCCTCGTTTTGATGGT 58.278 50.000 0.00 0.00 0.00 3.55
2398 7621 4.811557 CCTGAAATGAGATAACGTTCTCCC 59.188 45.833 2.82 0.00 41.24 4.30
2402 7625 4.271291 GCTCCCTGAAATGAGATAACGTTC 59.729 45.833 2.82 0.00 0.00 3.95
2405 7628 3.134458 GGCTCCCTGAAATGAGATAACG 58.866 50.000 0.00 0.00 0.00 3.18
2406 7629 3.134458 CGGCTCCCTGAAATGAGATAAC 58.866 50.000 0.00 0.00 0.00 1.89
2407 7630 2.485479 GCGGCTCCCTGAAATGAGATAA 60.485 50.000 0.00 0.00 0.00 1.75
2410 7633 1.221840 GCGGCTCCCTGAAATGAGA 59.778 57.895 0.00 0.00 0.00 3.27
2411 7634 1.821332 GGCGGCTCCCTGAAATGAG 60.821 63.158 0.00 0.00 0.00 2.90
2413 7636 3.204827 CGGCGGCTCCCTGAAATG 61.205 66.667 7.61 0.00 0.00 2.32
2431 7654 6.088350 GTGTCTAGCTTAGAAAAACGAGACAG 59.912 42.308 8.50 0.00 41.23 3.51
2444 7667 5.790593 TGTTAGGGTTTGTGTCTAGCTTAG 58.209 41.667 0.00 0.00 0.00 2.18
2446 7669 4.699925 TGTTAGGGTTTGTGTCTAGCTT 57.300 40.909 0.00 0.00 0.00 3.74
2451 7674 7.706100 TTAAGTTTTGTTAGGGTTTGTGTCT 57.294 32.000 0.00 0.00 0.00 3.41
2481 7704 6.821665 CGGTGGAAGGACTTCATTTTTAGATA 59.178 38.462 13.51 0.00 41.20 1.98
2483 7706 5.001232 CGGTGGAAGGACTTCATTTTTAGA 58.999 41.667 13.51 0.00 41.20 2.10
2484 7707 4.156008 CCGGTGGAAGGACTTCATTTTTAG 59.844 45.833 13.51 0.00 41.20 1.85
2493 7716 1.073199 CTTGCCGGTGGAAGGACTT 59.927 57.895 1.90 0.00 0.00 3.01
2495 7718 3.056328 GCTTGCCGGTGGAAGGAC 61.056 66.667 1.90 0.00 0.00 3.85
2496 7719 4.697756 CGCTTGCCGGTGGAAGGA 62.698 66.667 1.90 0.00 0.00 3.36
2524 7747 3.690685 TTAAGTCCATGGGGCGCGG 62.691 63.158 13.02 0.00 0.00 6.46
2533 7756 0.916809 CTCCGGGGGTTTAAGTCCAT 59.083 55.000 0.00 0.00 0.00 3.41
2534 7757 0.178897 TCTCCGGGGGTTTAAGTCCA 60.179 55.000 0.00 0.00 0.00 4.02
2535 7758 0.251354 GTCTCCGGGGGTTTAAGTCC 59.749 60.000 0.00 0.00 0.00 3.85
2536 7759 0.108472 CGTCTCCGGGGGTTTAAGTC 60.108 60.000 0.00 0.00 0.00 3.01
2537 7760 0.542702 TCGTCTCCGGGGGTTTAAGT 60.543 55.000 0.00 0.00 33.95 2.24
2538 7761 0.175073 CTCGTCTCCGGGGGTTTAAG 59.825 60.000 0.00 0.00 33.95 1.85
2539 7762 0.542702 ACTCGTCTCCGGGGGTTTAA 60.543 55.000 0.00 0.00 39.51 1.52
2549 7772 4.131088 GCCGGTCCACTCGTCTCC 62.131 72.222 1.90 0.00 0.00 3.71
2580 7803 2.577772 ATTAGGGTTCCTCTGCCTCT 57.422 50.000 0.00 0.00 34.61 3.69
2582 7805 2.250273 TCCTATTAGGGTTCCTCTGCCT 59.750 50.000 9.88 0.00 35.59 4.75
2597 7820 0.464554 GCAGCCGCCTTCTTCCTATT 60.465 55.000 0.00 0.00 0.00 1.73
2603 7826 0.253044 TCTTATGCAGCCGCCTTCTT 59.747 50.000 0.00 0.00 37.32 2.52
2609 7832 1.463831 CATGATCTCTTATGCAGCCGC 59.536 52.381 0.00 0.00 39.24 6.53
2616 7839 8.763356 GCTGTTTAGAAGACATGATCTCTTATG 58.237 37.037 0.00 0.00 36.27 1.90
2617 7840 8.481314 TGCTGTTTAGAAGACATGATCTCTTAT 58.519 33.333 0.00 0.00 36.27 1.73
2638 7861 9.139174 GTTATGTATGCTACAAAAATTTGCTGT 57.861 29.630 5.82 10.19 42.76 4.40
2684 7907 5.539582 TTACGTTTAGATGCCACATGAAC 57.460 39.130 0.00 0.00 0.00 3.18
2693 7916 9.944663 TCAATTCCAATATTTACGTTTAGATGC 57.055 29.630 0.00 0.00 0.00 3.91
2763 7987 9.558396 TTTTGCCTACAAAGAATCAAATTTGAT 57.442 25.926 24.83 24.83 46.33 2.57
2764 7988 8.954950 TTTTGCCTACAAAGAATCAAATTTGA 57.045 26.923 22.52 22.52 46.08 2.69
2765 7989 9.044150 TCTTTTGCCTACAAAGAATCAAATTTG 57.956 29.630 12.15 12.15 46.08 2.32
2766 7990 9.264719 CTCTTTTGCCTACAAAGAATCAAATTT 57.735 29.630 0.00 0.00 46.08 1.82
2767 7991 8.641541 TCTCTTTTGCCTACAAAGAATCAAATT 58.358 29.630 0.00 0.00 46.08 1.82
2768 7992 8.181904 TCTCTTTTGCCTACAAAGAATCAAAT 57.818 30.769 0.00 0.00 46.08 2.32
2769 7993 7.581213 TCTCTTTTGCCTACAAAGAATCAAA 57.419 32.000 0.00 0.00 46.08 2.69
2770 7994 7.094205 GGATCTCTTTTGCCTACAAAGAATCAA 60.094 37.037 0.00 0.00 46.08 2.57
2771 7995 6.375455 GGATCTCTTTTGCCTACAAAGAATCA 59.625 38.462 0.00 0.00 46.08 2.57
2772 7996 6.457528 CGGATCTCTTTTGCCTACAAAGAATC 60.458 42.308 0.00 0.00 46.08 2.52
2773 7997 5.355350 CGGATCTCTTTTGCCTACAAAGAAT 59.645 40.000 0.00 0.00 46.08 2.40
2774 7998 4.695455 CGGATCTCTTTTGCCTACAAAGAA 59.305 41.667 0.00 0.00 46.08 2.52
2775 7999 4.253685 CGGATCTCTTTTGCCTACAAAGA 58.746 43.478 0.00 0.00 46.08 2.52
2776 8000 3.375299 CCGGATCTCTTTTGCCTACAAAG 59.625 47.826 0.00 0.00 46.08 2.77
2777 8001 3.008594 TCCGGATCTCTTTTGCCTACAAA 59.991 43.478 0.00 0.00 43.97 2.83
2778 8002 2.569853 TCCGGATCTCTTTTGCCTACAA 59.430 45.455 0.00 0.00 0.00 2.41
2779 8003 2.184533 TCCGGATCTCTTTTGCCTACA 58.815 47.619 0.00 0.00 0.00 2.74
2780 8004 2.981859 TCCGGATCTCTTTTGCCTAC 57.018 50.000 0.00 0.00 0.00 3.18
2781 8005 3.433598 CCAATCCGGATCTCTTTTGCCTA 60.434 47.826 19.43 0.00 36.56 3.93
2782 8006 2.648059 CAATCCGGATCTCTTTTGCCT 58.352 47.619 19.43 0.00 0.00 4.75
2783 8007 1.678101 CCAATCCGGATCTCTTTTGCC 59.322 52.381 19.43 0.00 36.56 4.52
2784 8008 1.678101 CCCAATCCGGATCTCTTTTGC 59.322 52.381 19.43 0.00 36.56 3.68
2793 8017 1.379843 GTTGCCACCCAATCCGGAT 60.380 57.895 12.38 12.38 36.56 4.18
2816 8040 2.941480 AGGAGTACACTACCCATACGG 58.059 52.381 0.00 0.00 37.81 4.02


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.